Well, the real issue here is that you need libraries to make your work easier. JVM as a platform has many more options than PHP, if for no other reason than you can hybridize your application with embedded languages. Also, Hibernate is fantastic as an ORM (Object Relational Mapping), basically taking your tables and looking at them as POJOs.
If you're doing lots of 'raw' stuff, I actually like using Sequel, which is a Ruby library and works very well on JRuby. In general, I find that the duck-typing/concise code that people like about PHP is absolutely replicable in Ruby via JRuby (or Jython for you Python enthusiast types).
The best library is going to be dictated by the funkiness of the schema you're dealing with, in addition to the type of work you're doing. Do you need to do lots of complicated queries, fetching columns from several tables all at once? Or is it more along the lines of "I Need to fetch all the Orders for a certain customer and display it in an order history chart"? ORMs are better suited to the latter, which is what web apps tend to be, but your mention of parsing and analyzing makes me wonder if it's more the former.
Hibernate gives you the greatest flexibility, I find. It's not a good idea to use autogenerated stuff without reviewing it, but if you use Eclipse, there's a plugin that will generate the classes for you.
Another reason to go with Java: If you look at the Glassfish container for your web application, it has built in JDBC pools for you and you can look at the statistics and management of the pool. If you have a lot of database access, this could be pretty useful.